Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• pmid-41808025

  PMID 41808025 · PMC13085422 · 8 claims · 7 setups

  Full-text index only

  E2 exposure induces male-to-female gonadal sex reversal in CGS, confirmed by histological evidence across developmental stages.

  gonadal tail-tip deg candidate rna-seq histology rt-qpcr

• Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.

  PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 7 claims · 6 setups

  Has reproduction · 65

  UC patient-derived organoids histologically phenocopy primary UC tissue, showing disorganized stratified epithelium, reduced mucin/goblet cells, and non-uniform proliferation compared to non-IBD organoids

  patient-derived h3k27ac rna-seq chip-seq histology

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups

  Has reproduction · 78

  INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

  testis young testicular invade-seq histology sperm

• Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

  PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

  Has reproduction · 10

  Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

  testis dissociated epididymis chip-seq strand-specific h&e

• Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

  PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

  Has reproduction · 95

  Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

  kidney live blood snrna-seq snatac-seq bulk

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western

• Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

  PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 74

  RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

  pericarp green cuiguan illumina bulk qrt-pcr light

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

  PMID 41419303 · PMC13151493 · Gut · 2026 · 8 claims · 8 setups

  Full-text index only

  KC-Cpa1 mice show markedly increased pancreatic remodelling, fibrosis and metaplastic/PanIN lesion formation compared with KC mice

  pancreas cre acinar scrna-seq histology bulk single-cell

• Rete ridges form via evolutionarily distinct mechanisms in mammalian skin.

  PMID 41639458 · PMC12959975 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  Rete ridges form through a mechanism independent from hair follicles and sweat glands, via interconnected epidermal invaginations

  trunk pig multispecies gw12 histology comparative immunostaining

• A spatially resolved human glioblastoma atlas reveals distinct cellular and molecular patterns of anatomical niches.

  PMID 41714633 · PMC13031279 · Nature communications · 2026 · 8 claims · 6 setups

  Full-text index only

  GBM exhibits distinct cellular and molecular patterns organized by anatomical niche, with malignant, vascular, and immune compartments showing region-specific spatial associations

  gbm glioma single-cell scrna-seq cite-seq spatial

• Single-cell and spatial transcriptomics define 20E-driven developmental reprogramming in silkworm wing disc.

  PMID 41730863 · PMC13039787 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  Wing morphogenesis (Wm) cells act as central progenitors/differentiation hub, giving rise to epithelial and cuticle lineages under lineage-specific transcription factors

  mori spodoptera scrna-seq stereo-seq snrna-seq

• Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

  PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

  Has reproduction · 69

  Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

  colon gut single-cell 16s western

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 90

  Multi-omic profiling (snRNA-seq + spatial transcriptomics) of human sural nerves identifies novel cell type markers (MLIP in mySC; GRIK3, PRIMA1 in nmSC; CXCL14 in periC) not previously described in rodent or human literature

  sural peripheral snrna-seq nerve single-nucleus subcellular situ

• Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

  PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

  ucec ishikawa rna-seq proteomics immunohistochemistry

• The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.

  PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  SMCs show high gene expression for mucus-secreted proteins (Tff1, Gkn1, Gkn2, Psca, Muc5ac), mitoribosome RNA, and cytoskeleton proteins

  laser-microdissected gastric ffpe oct-embedded sequencing glycomics immunofluorescence

• An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

  PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

  liver hcv-infected serum bulk chip-seq serum

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

  Full-text index only

  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.

  PMID 41511606 · PMC12995935 · Applied biochemistry and biotechnology · 2026 · 8 claims · 8 setups

  Full-text index only

  TEAD4 and RXRA play critical roles in IDD progression, likely regulating NP cell behavior and ECM metabolism via the TNF-α/NF-κB pathway

  differential il-1β-induced scrna-seq bulk gsea

• Exploring phenotype-related single-cells through attention-enhanced representation learning.

  PMID 41566378 · PMC12906058 · Genome medicine · 2026 · 6 claims · 5 setups

  Full-text index only

  scPhase, an attention-based multiple instance learning (AMIL) framework with Mixture-of-Experts aggregation, predicts sample-level clinical phenotypes from raw scRNA-seq data and generalizes across patient cohorts

  pbmcs brain tumor scrna-seq